Robustness and parameter geography in post-translational modification systems

The Structure of MESSI Biological Systems

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Identifying parameter regions for multistationarity

(2017) Carsten Conradi et al.   PLoS Computational Biology

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling

(2017) Irene Otero-Muras et al.   PLoS Computational Biology

Long-term dynamics of multisite phosphorylation

(2016) Boris Y. Rubinstein et al.   MOLECULAR BIOLOGY OF THE CELL

Algebraic Systems Biology: A Case Study for the Wnt Pathway

(2015) Elizabeth Gross et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry

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Mixed mechanisms of multi-site phosphorylation

(2015) T. Suwanmajo et al.   Journal of the Royal Society Interface

An analytical approach to bistable biological circuit discrimination using real algebraic geometry

(2015) Dan Siegal-Gaskins et al.   Journal of the Royal Society Interface

MAPK’s networks and their capacity for multistationarity due to toric steady states

(2015) Mercedes Pérez Millán et al.   MATHEMATICAL BIOSCIENCES

Pervasive robustness in biological systems

(2015) Marie-Anne Félix et al.   NATURE REVIEWS GENETICS

A Fundamental Trade-off in Covalent Switching and Its Circumvention by Enzyme Bifunctionality in Glucose Homeostasis

(2014) Tathagata Dasgupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Catalytic constants enable the emergence of bistability in dual phosphorylation

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Injectivity, multiple zeros and multistationarity in reaction networks

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Multistationarity in Sequential Distributed Multisite Phosphorylation Networks

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Time-scale separation - Michaelis and Menten's old idea, still bearing fruit

(2013) Jeremy Gunawardena   FEBS Journal

Extracting insights from the shape of complex data using topology

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Algorithm 921

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Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization

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Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

The human hair follicle, a bistable organ?

(2012) Bruno A. Bernard   EXPERIMENTAL DERMATOLOGY

Realistic enzymology for post-translational modification: Zero-order ultrasensitivity revisited

(2012) Yangqing Xu et al.   JOURNAL OF THEORETICAL BIOLOGY

Some lessons about models from Michaelis and Menten

(2012) Jeremy Gunawardena   MOLECULAR BIOLOGY OF THE CELL

A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems

(2012) Jeremy Gunawardena   PLoS One

Characterizing Multistationarity Regimes in Biochemical Reaction Networks

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Simplifying the Jacobian Criterion for Precluding Multistationarity in Chemical Reaction Networks

(2012) Badal Joshi et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding

(2012) Sudhakaran Prabakaran et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The protein kinase Mζ network as a bistable switch to store neuronal memory

(2011) Hideaki Ogasawara et al.   BMC Systems Biology

Efficient characterization of high-dimensional parameter spaces for systems biology

(2011) Elías Zamora-Sillero et al.   BMC Systems Biology

Chemical Reaction Systems with Toric Steady States

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Sensitivity analysis approaches applied to systems biology models

(2011) Z. Zi   IET Systems Biology

Robust Network Topologies for Generating Switch-Like Cellular Responses

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Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

The scaffold protein Ste5 directly controls a switch-like mating decision in yeast

(2010) Mohan K. Malleshaiah et al.   NATURE

Robustness and Evolvability

(2010) Joanna Masel et al.   TRENDS IN GENETICS

Bistability in Apoptosis by Receptor Clustering

(2010) Kenneth L. Ho et al.   PLoS Computational Biology

Defining Network Topologies that Can Achieve Biochemical Adaptation

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Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

The rational parameterisation theorem for multisite post-translational modification systems

(2009) Matthew Thomson et al.   JOURNAL OF THEORETICAL BIOLOGY

Unlimited multistability in multisite phosphorylation systems

(2009) Matthew Thomson et al.   NATURE

Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks

(2009) Adel Dayarian et al.   PLoS Computational Biology

The Geometry of Multisite Phosphorylation

(2008) Arjun Kumar Manrai et al.   BIOPHYSICAL JOURNAL

Geometry and topology of parameter space: investigating measures of robustness in regulatory networks

(2008) Madalena Chaves et al.   JOURNAL OF MATHEMATICAL BIOLOGY

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE